MiAIRR "Lab" clarification... about airr-standards HOT 10 CLOSED

Just to be clear, I am referring to:

1 / study | Lab name
1 / study | Contact information (data collection)
1 / study | Contact information (data deposition)
1 / study | Lab address

from airr-standards.

My understanding was that the "lab" is related to the data submitter/contact person:
As you said
"the contact info for the data collection and data deposition are contact points within the lab for key aspects of the work"

from airr-standards.

I'm not sure this completely answers the question, but for NCBI submission at least the study <-> BioProject. In a BioProject submission, the first screen has submitter information. This would correspond to the "Contact information (data deposition" and "Lab address" fields, though note that NCBI does not have any field that corresponds explicitly to "Lab name".

Later on the submission process, there is the ability to indicate a data provider with the help saying "indicate the data provider (data submitter) if it is someone other than the submitting organization or consortium. For example, a sequencing center or a DACC." It would seem you could specify this scenario with "Contact information (data collection)". In the NCBI form, this is a free text field, plus an additional field to provide a URL.

from airr-standards.

Could we collapse these 4 fields into 2 (data collection & data deposition), which both contain:

• PoC name
• PoC email
• department
• institution
• full address

This way we would be most flexible, e.g. if a consortium has a centralized facility for data submission that could belong to a different institution.

from airr-standards.

I assume that the intent is that through these fields we are providing the principal contact point for a study (there is no other mechanism for this at the moment). If so, which one of these is the principal contact. Or should there be three, the principal lab/contact person (the "corresponding author" so to speak), the data collection lab, and the data submission lab? In the iReceptor world, we have a principal lab and contact, but not separate information for data collection and data submission. I am trying to figure out which is the principal contact point for the study from the current fields. This is unclear to me at the moment.

iReceptor allows you to group/aggregate study/data views based on lab. For example, you could look at all of the studies where the "Kleinstein Lab" was the "data collector" (assuming there was such data in a repository). I am trying to determine which "lab" entity in the Minimal Standards our principal lab aggregation should relate to.

Should there be another group of entities in the Minimal Standard about being the principal contact for the study itself (as opposed to data collection and data submission which could be different). Or is what we have enough?

Brian

from airr-standards.

The "collecting" lab / PoC would be the principal contact for the study. The "submitting" PoC is mainly provided to quickly resolve technical issues with the submission itself.
IIRC we discussed the trichotomy (corresponding/collecting/submitting) you mentioned, but decided that for nearly all purposes (sample requests, legal compliance, etc.) "collecting" could be considered a subcontractor of "corresponding", so we did not include it. In case there is any scenario in which this would be important, we should discuss again.

from airr-standards.

OK, this seems more clear...

One other question - the standard states that the "Contact information (data collection)" field has a content type of "RFC6530-compliant email address". This seems restrictive, in that there is no ability to put something like "Brian Corrie ([email protected])" as the contact information. Was the intent of this field to enforce it to be an email address and only an email address? That is how I interpret the "content type" as it stands now.

from airr-standards.

I think the idea here was that Lab name, Lab address and Contact information (data collection) would all refer to the same group/institution, so that in the contact field we wanted to make sure that there is a valid e-mail address on file (assumed to belong to the PI). If we go for the dichotomy (collecting/submitting) we discussed, then each of the two fields would become free text again, containing the five items listed above.

from airr-standards.

The definitions have been amended and slightly changed in 8f63c1e, but otherwise the four fields are still in v0.1. I will close this issue, if you want to have it on the MiAIRR v2 change list, please reopen it.

from airr-standards.

I have a vague memory that not all possible contacts were included in the minimal standards template because of 'the minimalism'

from airr-standards.